Temperate grain legumes, including faba bean, field pea, chickpea, lentil, and grass pea, are important food and forage crops in the cereal-based cropping system in the Nile Valley and Red Sea region countries. Despite their importance, local production remains insufficient, and the countries are forced to import to narrow the demand gaps. Emerging diseases, such as faba bean gall disease and several viruses (Chickpea chlorotic dwarf virus, Chickpea chlorotic stunt virus, Faba bean necrotic yellows virus, and Pea seed-borne mosaic virus), are on the rise due to climate variability, changes in farming systems such as monocropping, reduced crop rotations, limited knowledge about the pathogens, and absence of varieties with good levels of resistance. This review synthesizes research achievements in the region and identifies focus areas, primarily resistance breeding, characterization of pathogen populations, developing efficient screening techniques, investigations of mixed virus infections, advancement of pathogen diagnostic techniques, and developing agroecologically based disease management strategies to reduce economic impacts of new and re-emerging diseases. Moreover, research collaboration and information exchange among countries in the region are essential to mitigate the growing threat of emerging legume diseases.

Yam (Dioscorea spp.) is a major staple crop in West and Central Africa, but its productivity remains limited by the underutilization of available genetic diversity. This study evaluated the agro-morphological diversity and population structure of cultivated yams in Cameroon. A total of 224 accessions were collected from farmers’ fields and local markets across major yam-growing regions and established in an on-farm trial at the International Institute of Tropical Agriculture (IITA), Yaoundé, using a serpentine design without replication. A subset of 126 accessions, representing four healthy plants per landrace and sampling locality, was characterized using 42 agro-morphological descriptors encompassing tuber, vegetative, and inflorescence traits. Data were standardized using z-score transformation and analyzed using principal components analysis (PCA) for exploratory ordination. Based on PCA ordination, accessions with similar local names were aggregated to reduce the dataset to 88 landraces. Mean trait values were subjected to Gower distance-based hierarchical clustering. The first two principal components explained 45.4

Yams (Dioscorea spp.) are an important vegetatively propagated food security crop grown for their starchy tubers. Yams are susceptible to several viruses, and their genomes harbor a diverse array of endogenous pararetroviral sequences (EPRVs), which complicate diagnostics and germplasm exchange because of their similarity to episomal viruses. To better characterize EPRV diversity, we analyzed 86 publicly available whole-genome sequences from five Dioscorea species (D. rotundata, D. alata, D. praehensilis, D. abyssinica, and D. dumetorum). Assembled genomes were screened for endogenous pararetrovirus sequences (EPRVs) using the CAULIFINDER pipeline, targeting conserved RT/RNase H domains of the Caulimoviridae family. Our analyses revealed four major EPRV groups in D. rotundata: Yendovirus, Badnavirus, Yam Endovirus 1, and a Dioscovirus-like lineage. While most insertions were fragmented, we found full-length putative viral genomes corresponding to the Yam Badnavirus and Dioscovirus-like clades. These findings expand knowledge of yam EPRV diversity, contribute to the development of improved diagnostic tools to differentiate endogenous and episomal forms, and promote a science-based, risk-proportionate approach to yam phytosanitation that facilitates global germplasm exchange while maintaining biosecurity.

Abstract Banana bunchy top virus (BBTV) continues to threaten smallholder livelihoods and food security across sub-Saharan Africa. While clean-seed programmes are widely promoted, their long-term effectiveness is often compromised by rapid reinfection in endemic landscapes. We developed an integrated framework combining spatially explicit, stochastic epidemiological modelling with additional cost–benefit analysis and use of socio-behavioural data to evaluate strategies for stabilising production. Our results demonstrate that frequent monthly inspections and accurate symptom detection are essential for disease suppression. Crucially, the economic analysis reveals that prioritizing diagnostic competence as an economic asset is necessary: improving detection efficiency can more than double farmer net revenue under realistic market conditions. Socio-behavioural findings further confirm that a farmer’s ability to correctly recognise symptoms is the strongest predictor of roguing adoption, far outweighing demographic characteristics. These results provide quantifiable guidance for disease management and highlight that the sustainability of clean-seed interventions hinges on shifting policy from simple seed replacement to investing in farmer diagnostic capacity. Strengthening this local surveillance capability transforms informal seed systems into resilient, durable tools for safeguarding household nutrition and regional food security.

OBJECTIVE: This study narrows this knowledge gap by estimating the effect of the quantity of certified seeds produced and the spatial variations where they are produced on the use of certified seeds and yields. We also assess the yield effects of certified seeds use and their relationship with agroclimatic and socioeconomic conditions. METHODS: We combine nationally-representative farm-household survey panel data with spatial data on the headquarters locations of seed companies, the quantity of certified seeds for maize, cowpea, and rice that they produce, and spatially explicit agroecological data. We apply panel fixed effects methods as well as instrumentalvariable methods to address potential endogeneity associated with certified seeds use while also controlling for the use of improved varieties to separate their effects from the effects of certified seeds. RESULTS AND CONCLUSIONS: Our findings indicate that the availability of certified seeds-captured by indicators of certified seeds produced by seed companies headquartered in the states of survey respondents-is associated with positive but declining marginal effects on certified seeds use and yields. These results are robust when we also consider the potential within-state heterogeneity in the proximity to seed company headquarters, as well as potential spillovers from the nearest adjacent states. The yield effects of certified seeds are heterogeneous and depend on agroclimatic conditions and farmers' socioeconomic characteristics. The use of certified seeds is somewhat higher in areas with higher yield effects after controlling for certified seeds production. These to be used by farmers with higher expected returns than farmers with lower expected returns. These results African country that returns to seed certification systems in the current setting significantly vary depending on

Cassava is a vital food security crop grown in the tropics primarily for its starchy tuberous roots that play a significant role in calorie intake in Africa. The cassava seed system has been historically neglected resulting in the widespread propagation of poor quality and diseased planting materials (stems/cuttings). Recently there have been ongoing efforts to modernise cassava breeding and improve seed delivery in Tanzania which have resulted in the creation of a functional and commercially sustainable cassava seed system. This system comprises a decentralized network of seed producers in a hierarchy from early generation to community-based seed with different quality assurance requirements at each level. Seed entrepreneurs are registered on a ‘SeedTracker™' database where volumes of seed produced can be tracked for each variety. In this study, we analysed SeedTracker™ data and household survey data to determine the Weighted Average Varietal Age (WAVA) of improved cassava varieties in Tanzania. We used total seed (cuttings) produced as weights for WAVA estimations. Results showed changes in WAVA from 11.3 years in 2018, 13.6 years in 2019, 13.5 years in 2020, 10.6 years in 2021, 11.4 years in 2022 to 10.1 years in 2023. This suggests that there is an accelerating turnover rate of improved cassava varieties. The findings of this study are useful to cassava seed system actors such as policymakers, quality assurance agencies, breeders, and seed businesses. This study also serves as an indicator of the positive impacts being achieved through cassava seed system interventions in the country. Furthermore, it validates the adopted cassava seed system model and suggests that the model could be readily adapted to other crop systems where varieties are being routinely monitored.

Summary Societal Impact Statement Banana and plantain are critical for food security and income generation in West Africa, particularly for smallholder farmers in countries such as Benin. However, banana bunchy top virus (BBTV) poses a major threat to sustainable production. This study integrates high-resolution remote sensing, field epidemiology, mathematical modelling, and socioeconomic analysis to improve understanding of the spread of BBTV and to evaluate the effectiveness of different disease control strategies. Our findings reveal that BBTV risk is highest in southern Benin, where socioeconomic vulnerability is also greatest. Low disease awareness, limited adoption of effective control methods and informal exchange of planting material exacerbate this risk. By identifying priority areas and strategies tailored to local social, economic, and agroecological contexts, this research offers a roadmap for designing targeted, sustainable BBTV management programs. These insights can support smallholder resilience, reduce disease burden, and safeguard banana-based livelihoods across sub-Saharan Africa. ### Competing Interest Statement The authors have declared no competing interest. Bill & Melinda Gates Foundation, https://ror.org/0456r8d26, INV070408, INV010652

Cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are the two main viral diseases threatening cassava production in the Democratic Republic of the Congo (DRC). CMD can be effectively controlled using resistant varieties; however, currently, there are no cassava varieties that exhibit durable resistance to CBSD. As the deleterious effects of CBSD become more pronounced with the maturity of the cassava, we assessed the potential benefits of early harvesting on mitigating the impact of CBSD on the performance of two improved CMD-resistant cassava varieties, Nabana (MM 96/4653) and Sawasawa (MM 96/3920). The percentage yield reduction was calculated by comparing the yield of infected treatments to that of uninfected treatments. At 9 months after planting (MAP) and 12 MAP, overall fresh root yield from farmer-selected healthy planting material of varieties Nabana and Sawasawa was significantly higher than the yield of crops established using CBSD-infected cuttings of the same varieties. Fresh root yield losses due to CBSD for Nabana were 44% at 9 MAP and 86% at 12 MAP, while for Sawasawa, they were 40% at 9 MAP and 72% at 12 MAP. Healthy planting material of the two varieties yielded 5% more at 12 MAP than at 9 MAP, while infected planting material yielded 52.5% less at 12 MAP than at 9 MAP. These results highlight the benefits of using healthy planting material in conjunction with early harvesting to minimize losses among CBSD-susceptible cassava varieties. These results suggest the need for a robust seed system that can deliver disease-free planting material of market-preferred varieties to farmers, thereby promoting food security.

Societal Impact Statement Banana and plantain are vital for food security and income in West Africa, yet banana bunchy top virus (BBTV) threatens production. This study combined remote sensing, field surveys, modelling and socio‐economic analysis to assess BBTV spread and control strategies in Benin. We found that risk is highest in southern regions with low disease awareness, limited adoption of control measures and widespread informal planting material exchange. By identifying priority areas and context‐specific interventions, our findings provide actionable guidance for targeted BBTV management, supporting smallholder resilience, reducing disease impact and safeguarding livelihoods across sub‐Saharan Africa. Summary This study investigates banana bunchy top virus (BBTV), a major threat to banana and plantain production in Benin, which are critical for food security and income for smallholder farmers. We combined remote sensing, field surveillance, household surveys and mathematical modelling to map banana cultivation; detect BBTV prevalence; and evaluate control strategies. BBTV was detected in 140 of 747 fields, with the highest prevalence in southern humid regions; modelling showed that injection was the most effective nationally, while uprooting was the most effective in high‐risk, socio‐economically vulnerable areas. Our findings highlight the need for context‐specific, spatially targeted interventions integrating clean planting materials, farmer education and epidemiologically informed management to enhance smallholder resilience and safeguard livelihoods.

Vegetatively propagated crops such as cassava, potato, sweetpotato, and yam, or roots and tubers (RTs), play a major role in food security in low- and middle-income countries, yet phytosanitary issues in the tropics lead to substantial yield and quality losses. Challenges to production include institutional limitations that prevent effective responses and potential buildup of pathogens during clonal propagation. Addressing these challenges in a climate change context and diverse sociocultural environments requires a multifaceted approach, including improving access and availability to clean seed by strengthening seed systems; breeding for host resistance and disseminating resistant varieties; strengthening on-farm seed management; and designing effective policies and regulations to deal with seedborne diseases. Vital cross-cutting activities that can help to tackle the phytosanitary challenges of RTs include capacity strengthening, research on emergent pathogens, and improving regional cooperation and harmonization of phytosanitary standards to manage transboundary seed movement.

In the 15 years since High Throughput Sequencing (HTS) was first used for the detection and identification of plant viruses, the technology has matured and is now being used in frontline plant biosecurity applications. Anticipating the challenges this new approach was starting to reveal, recommendations were made a decade ago to streamline the application of these technologies. The recommendations were (1) for countries to increase baseline surveillance, (2) to address nomenclature for “data inferred” new viral sequence to differentiate from characterised viruses, and (3) to increase the focus on fundamental biological research to deal with the deluge of new discoveries. Here, we review the progress made on these recommendations in the intervening decade and discuss the anticipated future challenges posed by the broader adoption of HTS in routine biosecurity applications, especially as we move towards a potential asymptote in the rate of virus discovery. The three initial recommendations are still relevant, however, the decade of discovery and development has led to a change in approaches and ways of thinking. A fourth recommendation is made here, to reduce the biosecurity risks through equal inclusion and access to research and technology, locally and globally. This equality will create increased consonance between community members, researchers, risk analysts, biosecurity authorities, and policy makers at national and international levels and a step change reduction of biosecurity incursions of phytopathogenic viruses.

An isolate of a novel begomovirus, named eggplant yellow mosaic virus (EYMV), was molecularly characterized from a naturally infected, field-collected eggplant exhibiting yellow mosaic symptom in Iguowan, Edo State, Nigeria. Its complete monopartite genome is 2,805 nucleotides (nt) long, containing two virion-sense (V1 and V2) and four complementary-sense (C1-C4) open reading frames. In pairwise comparisons, EYMV shared the highest (86%) genome sequence identity with tomato leaf curl Cameroon virus isolate GH-Tou-12. Phylogenetic analysis showed that EYMV belonged to the same clade as okra yellow crinkle virus (OYCrV). Further analysis revealed the recombinant nature of EYMV, with the potential major and minor parental viruses being OYCrV and tomato leaf curl Nigeria virus, respectively. The species name "Begomovirus melongenaflavi" is proposed for EYMV.

Metarhizium anisopliae (Metschnikoff) Sorokin and Beauveria bassiana (Balsamo) Vuillemin are entomopathogenic fungi commonly used in microbial control of arthropods. In this study, we evaluated the insecticidal potential of six isolates of B. bassiana (BIITAC10.3.3, BIITAC6.2.2, and BIITAC8.1.5) and M. anisopliae (MIITAC11.3.4, MIITAC6.2.2, and MIITAC6.4.2) from Cameroon, against the banana aphid Pentalonia nigronervosa Coquerel, the vector of the banana bunchy top virus (BBTV). Pathogenicity tests were initially conducted using B. bassiana and M. anisopliae isolates at a concentration of 3.2 × 106 conidia/ml on P. nigronervosa adults sourced from four agroecologies in Cameroon. Four isolates (BIITAC6.2.2, BIITAC10.3.3, BIITAC8.1.5, and MIITAC6.2.2) were highly pathogenic, causing greater than 75% aphid mortality in all populations. A significant decrease in aphid fecundity was observed with BIITAC6.2.2, MIITAC6.2.2, and BIITAC10.3.3. These three isolates were in a test of a series of four fungal concentrations (3.2 × 101, 3.2 × 102, 3.2 × 104, and 3.2 × 106 conidia/ml). produced LC50 of 1.31 × 101 and 3.12 × 10-2 for BIITAC10.3.3 and MIITAC6.2.2, respectively. MIITAC6.2.2 had the lowest LC90 (1.55 × 103). Our results strongly support the continued development of biopesticides based on one or more of the three fungal entomopathogens for the control of banana aphids as a component of an Integrated Pest Management (IPM) strategy for the reduction of the prevalence and transmission of BBTV under field conditions.

Invasions of arthropod vectors and viruses are the main factors associated with emerging plant viral diseases. The presence of the Banana bunchy top virus (BBTV, genus Babuvirus), an aphid-transmitted virus responsible for the banana bunchy top disease (BBTD), was first confirmed in 2008 in the South region of Cameroon. This study reports on surveys over 14 years to determine the status of BBTV spread and virus diversity in Cameroon. A total of 544 fields extending through 81 districts in 7 regions were surveyed in 5 phases: (1) 2009-10, (2) 2012, (3) 2013-14, (4) 2016-17, and (5) 2022. BBTV was detected in 36 sites, all located in the Ambam district in the South region, with an incidence in the virus-affected fields ranging from 5% to 40%, with an average incidence of 14.8%. The findings indicate BBTV expansion from the location of first detection in 2008 to about 4-25 km in all directions, with the virus spread range of about 700 km2, as of the last survey in 2022. Phylogenetic analysis using complete nucleotide sequences of the BBTV-R and BBTV-S gene aligned Cameroon isolates with the sub-Saharan Africa subgroup of the Pacific-Indian Oceans (PIO) group of BBTV isolates, suggesting a likely virus invasion from neighbouring central African countries where BBTV presence had been reported in the 1980s. Knowledge of BBTV distribution provided through the detection and delimiting surveys has contributed to the efficient targeting of interventions to limit the expansion of an emerging virus threat to banana production in Cameroon.

Genetic diversity is crucial for conservation efforts as well as breeding programs targeted at the development of improved varieties. Taro, a climate-resilient crop, plays a vital role in the nutritional and economic livelihoods of many households in Nigeria, but its yield is very low due to inadequate genetic improvement efforts. A diversity assessment of Nigerian taro is therefore required to create a premise for its improvement in yield, quality and disease tolerance. In this study, the genetic diversity and population structure of 490 taro cultivars comprising two main gene pools: Dasheen (215) and Eddoe (275), collected from farmers and marketers across seven states in Nigeria was assessed using 3047 Diversity Array Technology single nucleotide polymorphism (DArT-SNP) markers. A subset of 114 taro cultivars, comprising 30 Dasheens and 84 Eddoes were further phenotyped using 24 agro-morphological descriptors. Both phenotypic and molecular characterization revealed higher genetic diversity among the Eddoes than Dasheens. Estimates of gene flow (Nm = 0.353) revealed intermixing of cultivars among the States of collection, with the highest gene flow occurring between cultivars from Anambra and Ondo states and the lowest between Anambra and Kwara states. Population structure and Ward’s minimum variance hierarchical cluster based on DArT-SNPs identified four groups, one comprising Dasheen and three comprising Eddoe cultivars. Hierarchical clustering based on phenotypic traits delineated three clusters. Variation between gene pools (49

Seed transmission (ST) plays an important role in virus dispersion and disease epidemiology. Many viruses infecting cowpea are known to be seed-transmitted. This study evaluated the rate of virus ST in cowpea varieties inoculated under screenhouse conditions (SC) with bean common mosaic virus-blackeye cowpea mosaic strain (BCMV-BlCM), Southern bean mosaic virus (SBMV) and cucumber mosaic virus (CMV) under single and multiple-infections. Up to 50 seeds harvested from the virus-infected plants of each variety per treatment were used for the grow-out test under insect-proof SC. Data were recorded on seed germination (SG), symptoms in seedlings, and virus ST. The leaf samples were tested for viruses by enzyme-linked immunosorbent assay (ELISA) and reverse-transcription polymerase chain reaction (RT-PCR). The SG rate was 78 ± 2.8–100 ± 0

African yam bean (AYB) (Sphenostylis stenocarpa (Hochst ex. A. Rich.) harms) an underutilized legume that produces nutritionally healthy seeds and tubers in some variety. The low yield of the crop is attributed to production constraints such as attacks by pest and disease-causing organisms such as fungi, bacteria and viruses. In this study, one hundred AYB accessions were evaluated for resistance to viral infection. The AYB accessions were planted using a randomized complete block design on the experimental field at the International Institute of Tropical Agriculture (IITA) Ibadan, Nigeria. Viral disease severity was assessed at 10, 12, 14, 16 and 18 weeks after planting (WAP) based on disease symptoms using disease severity index on visual scale of 1–5. Antigen–coated plate enzyme linked immunosorbent assay (ELISA) and reverse transcription polymerase chain reaction were used to index diseased leaf samples collected from the field. Result from five virus species (Cowpea mild mottle virus, Cowpea mottle virus, Southern bean mosaic virus, Cowpea mosaic virus and Bean common mosaic virus) were detected in few accessions while mixed infections were observed in some accessions. TSs-552, TSs-577, TSs-580, TSs-560 and TSs-600 were devoid of viruses and could be resistant. There were no significant differences at p < 0.05 in the mean disease incidence (DI) of viral diseases. However, at 18 weeks after planting, TSs-604 had the highest (100%) mean DI while TSs-584 had the lowest (13.33%) mean DI. Cluster analysis based on the AUDPC produced 6 main clusters, the clusters revealed grouping patterns in which AYB lines with similar resistance ratings were shown to form unique clusters. The information generated from this study will contribute to the development of strategies in the management of virus diseases infecting AYB.

Cacao (Theobroma cacao L.) is a tropical tree species belonging to the Malvaceae, which originated in the lowland rainforests of the Amazon. It is a major agricultural commodity, which contributes towards the Gross Domestic Product of West African countries, where it accounts for about 70% of the world’s production. Understanding the genetic diversity of genetic resources in a country, especially for an introduced crop such as cacao, is crucial to their management and effective utilization. However, very little is known about the genetic structure of the cacao germplasm from Sierra Leone and Togo based on molecular information. We assembled cacao germplasm accessions (235 from Sierra Leone and 141 from Togo) from different seed gardens and farmers’ fields across the cacao-producing states/regions of these countries for genetic diversity and population structure studies based on single nucleotide polymorphism (SNP) markers using 20 highly informative and reproducible KASP–SNPs markers. Genetic diversity among these accessions was assessed with three complementary clustering methods, including model-based population structure, discriminant analysis of principal components (DAPC), and phylogenetic trees. STRUCTURE and DAPC exhibited some consistency in the allocation of accessions into subpopulations or groups, although some discrepancies in their groupings were noted. Hierarchical clustering analysis grouped all the individuals into two major groups, as well as several sub-clusters. We also conducted a network analysis to elucidate genetic relationships among cacao accessions from Sierra Leone and Togo. Analysis of molecular variance (AMOVA) revealed high genetic diversity (86%) within accessions. A high rate of mislabeling/duplicate genotype names was revealed in both countries, which may be attributed to errors from the sources of introduction, labeling errors, and lost labels. This preliminary study demonstrates the use of KASP–SNPs for fingerprinting that can help identify duplicate/mislabeled accessions and provide strong evidence for improving accuracy and efficiency in cacao germplasm management as well as the distribution of correct materials to farmers.

Phenotyping yam (Dioscorea spp.) germplasm for resistance to parasitic nematodes is hampered by the lack of an efficient screening method. In this study, we developed a new method using rooted yam vine cuttings and yam plantlets generated from semi-autotrophic hydroponics (SAHs) propagation for phenotyping yam genotypes for nematode resistance. The method was evaluated using 26 genotypes of D. rotundata for their reaction to Scutellonema bradys and four root-knot nematode species, Meloidogyne arenaria, M. enterolobii, M. incognita, and M. javanica. Yam plantlets established in nursery bags filled with steam-sterilized soil were used for screening against single nematode species. Plants were inoculated four weeks after planting and assessed for nematode damage eight weeks later. A severity rating scale was used to classify genotypes as resistant, tolerant, or susceptible determine based on the nematode feeding damage on tubers and the rate of nematode multiplication in the roots of inoculated plants. The results demonstrated putative resistance and tolerance against S. bradys in 58% of the genotypes and 88%, 65%, 65%, and 58% against M. arenaria, M. javanica, M. incognita, and M. enterolobii, respectively. The method is rapid, flexible, and seasonally independent, permitting year-round screening under controlled conditions. This method increases the throughput and speed of phenotyping and improves the selection process.